Renormalization group method in the singular perturbation theory, originally introduced by Chen et al, has been proven to be very practicable in a large number of singular perturbed problems. In this paper, we will firstly reconsider the Renormalization group method under some general conditions to get several newly rigorous approximate results. Then we will apply the obtained results to investigate a class of second order differential equations with the highly oscillatory phenomenon of highly oscillatory properties, which occurs in many multiscale models from applied mathematics, physics and material science, etc. Our strategy, in fact, can be also used to analyze the same problem for related evolution equations with multiple scales, such as nonlinear Klein-Gordon equations in the nonrelativistic limit regime.